Abstract
Many enteric viruses are found in pig farms around the world and can cause death of animals or important production losses for breeders. Among the wide spectrum of enteric viral species, porcine Sapelovirus (PSV), porcine Kobuvirus (PKoV) and porcine Astrovirus (PAstV) are frequently found in pig feces. In this study we investigated sixteen pig farms in Corsica, France, to evaluate the circulation of three enteric viruses (PKoV, PAstV-1 and PSV). In addition to the three viruses studied by RT-qPCR (908 pig feces samples), 26 stool samples were tested using the Next Generation Sequencing method (NGS). Our results showed viral RNA detection rates (i) of 62.0% [58.7-65.1] (n = 563/908) for PSV, (ii) of 44.8% [41.5-48.1] (n = 407/908) for PKoV and (iii) of 8.6% [6.8-10.6] (n = 78/908) for PAstV-1. Significant differences were observed for all three viruses according to age (P-value = 2.4e-13 for PAstV-1; 2.4e-12 for PKoV and 0.005 for PSV). The type of breeding was significantly associated with RNA detection only for PAstV-1 (P-value = 9.6e-6). Among the 26 samples tested with NGS method, consensus sequences corresponding to 10 different species of virus were detected. This study provides first insight on the presence of three common porcine enteric viruses in France. We also showed that they are frequently encountered in pigs born and bred in Corsica, which demonstrates endemic local circulation.
Highlights
Pig farms make an important contribution to the economy of world agriculture and are an important source of food
A very broad spectrum of viruses that can cause porcine diarrhea has been found in pig feces, including porcine Sapelovirus (PSV), porcine Kobuvirus (PKoV), porcine Sapovirus, porcine Astrovirus (PAstV), porcine Bocavirus and porcine Rotavirus [1,2,3,4,5,6,7]
We collected 919 pig feces samples from 16 pig farms selected according to location and breeding system
Summary
Pig farms make an important contribution to the economy of world agriculture and are an important source of food. Porcine diarrhea can cause mortality in animals, especially in piglets, and cause economic losses to the pig farmers; many of the pathogens responsible can infect humans. A very broad spectrum of viruses that can cause porcine diarrhea has been found in pig feces, including porcine Sapelovirus (PSV), porcine Kobuvirus (PKoV), porcine Sapovirus, porcine Astrovirus (PAstV), porcine Bocavirus and porcine Rotavirus [1,2,3,4,5,6,7]. Detection of porcine enteric viruses among pig farms
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